Wednesday, April 16, 2014

Another good one

Because I show a "level of intricacy in my work" which makes the journal "even more proud", they believe that my works "should be known to the mankind of science". Aha. No idea why I should "capitulate" my manuscript though. In terms of the language, this is one of the worst journal spam messages I have ever seen. Perhaps the chap who runs this business from a garage in Pakistan or Nigeria or whatever should consider taking an introductory English course before pretending to be a scientific publisher?

Oh, and peer review of only seven days from submission to publication? Yeah, right...

Tuesday, April 15, 2014

Is phylogenetic diversity flawed?

As indicated in my previous post on phylogenetic diversity (PD), what I really want to discuss is a recent paper, Kelly et al. (2014), that casts doubt on the utility of PD for conservation decisions. Again, understanding what this is about will require some excurses and explanations, but as we will see the main point is ultimately surprisingly banal.

As illustrated with the example of many species of grasses versus fewer species of oaks, lilies, grasses and ferns, the background is that PD is supposed to provide a metric for a form of diversity that we want to conserve. Now many of us would say that this form of diversity is evolutionary distinctness and be happy; we intuitively consider isolated lineages to be worthy of special protection. However, PD is often advertised as a proxy of what Kelly et al. call "feature diversity" (subsequently FD). That is, what we want to conserve in an area is not phylogenetic diversity per se but instead maximum diversity of some (morphological? ecological? genetic?) features. However, it is assumed that the more distant two species are in their evolutionary relationships, the more different they are likely to be in any given feature, and that is why we assume that high PD means high diversity of conservation relevant features.

Kelly et al. set out to test this assumption. Maybe one of their thoughts was that it may not actually be true because of convergence. One could argue that it doesn't make a lot of difference whether we protect a grass in the Poaceae family as long as there is a very similar looking grass-like Cyperaceae around. They have converged on the same ecological niche, so same thing really, right? But that is already the interpretation, perhaps it behoves me to stay with the methodology for the moment.

Friday, April 11, 2014

Phylogenetic diversity

Yesterday we discussed in our local journal club a recent paper arguing that the concept of phylogenetic diversity is flawed, or at a minimum not useful as a proxy for what the authors call "feature diversity".

Obviously to make sense of what I just wrote, a bit of background is needed. I will therefore use this post to explain what phylogenetic diversity is, and then discuss the actual problem (if there is one) the next time.

Thursday, April 10, 2014

Botany picture #152: Mentha requenii

Due to a conversation with somebody at work, the true mints have recently featured on my mind. They have always been one of my favourite genera, and I actually had a nice collection of species and hybrids on my balcony before I came to Australia. Due to quarantine restrictions, I had to leave them all behind and gave them away to colleagues. This one is rather unusual Mentha requienii (Lamiaceae), a very small, creeping species with a pungent minty scent. The picture was taken in 2009 in a botanic garden in Europe; unfortunately I don't remember which.

Tuesday, April 8, 2014

Character optimisation in parsimony phylogenetics

As mentioned in my last post on parsimony analysis, there are different forms of parsimony that are used in the reconstruction of phylogenetic relationships. We could describe them as different ways of counting the necessary number of character changes to explain a given phylogenetic tree.

Monday, April 7, 2014

Botany picture #151: Tagetes lemmonii

Tagetes lemmonii (Asteraceae), Royal Botanic Gardens of Sydney, 2011. This species comes from North America and is apparently a popular ornamental in some areas. What I found particularly striking about it was the pungent aromatic smell of the foliage; I am always fond of aromatic shrubs, probably because I worked on a genus of Lamiaceae in my Ph.D. project.

Friday, April 4, 2014

An addendum on Zander's Framework

Back in January and February I wrote a few posts on Richard Zander's A Framework for Post-Phylogenetic Systematics while I was reading the book:

Why we don't consider supraspecific taxa to be ancestral

No arguments from authority please, even if it is Charles Darwin

Two possible meanings of the term "pseudoextinction"

Can parsimony analyses be mislead by 'budding' speciation?

Can we trust molecular phylogenetics?

Although I admit that my reading got a bit less attentive towards the end, partly due to the rather repetitive style of the work, I considered myself to be done with the book. Today on the bus, however, I took it with me to deposit it on the bookshelf at work, and while stuck in a traffic jam I read once more over the chapter titled Contributions of Molecular Systematics.

On page 58, Zander argues that one should assign a support value to entire phylogenetic trees (which he strangely insists on calling cladograms although most of them have branch lengths):
Whole cladograms are seldom provided with confidence intervals (here including posterior probabilities) that reflect their perceived chance of being correct. In the literature, however, many cladograms are used in their entirety to model broad conclusions, e.g., many genera grouped into multiple families. These cladograms are commonly viewed as "mostly correct." But what does "mostly correct" mean? The binominal confidence interval (BCI) is here advanced to provide a measure of confidence in whole cladograms that are used for broad conclusions. It provides the proportion of nodes (or internodes) with Bayesian support measures that one can expect to be correct all at once than total nodes being correct at once, defining "correct" as joint probability of at least 0.99.
Maybe it is a language issue because I am not a native speaker of English, but my understanding of what the terms "confidence interval" and "to model" mean differs from how they are used here, and the last sentence does not appear to be complete. After mentioning some example numbers, he continues as can be expected:
Therefore, for most cladograms that are published and used for broad conclusions, the confidence in those cladograms, each used as a whole, seldom reaches 0.95, a standard for confidence in statistics.
I have given this issue some thought and I really do not understand why I should care about the overall support for the phylogeny as a whole. A simple thought experiment should get the point across.